Ligand pocket

Fig. 19.1 Schematic views of the ligand pocket of an enzyme, a Two adjacent pockets, each occupied by a needle fragment, b One large cavity that may be filled by two needle fragments.

GuiUoux VL, Schmidtke P, Tuffery P (2009) Fpocket an open source platform for ligand pocket detection. BMC Bioinformatics 11 1-11... 

Several ofher lipocalins whose tertiary structures have been elucidated adopt a very similar fold. These were dubbed prototypic lipocalins [21] in order to distinguish fhem from more distantly related members of fhe family [18]. Wifhin fhis subset, especially fhe / -barrel with the attached a-helix is highly conserved. In contrast, fhe four loops that form fhe entrance to fhe ligand pocket vary considerably in sequence, conformation, and length, fhus effecting fhe differing ligand specificities (Fig. 8.2). 

During these experiments the randomized residues were still restricted to the original set of positions chosen within the four loops. However, from recent structural analyses (see Section 8.4) it appeared that there are additional, so far non-mutated amino acids that contribute to the shape of the ligand pocket and may therefore govern affinity and specificity for the steroids. Thus, future improvement in molecular recognition by this engineered lipocalin may be guided by rational principles. 

In this chapter, we will describe the progress toward the implementation and the gradual improvement of such an engine, the arising challenges, and the approaches to address them. The collection of experimentally determined ligand pockets have been... 

Table XXVI summarizes two different series of wcio-tetraphenylporphyrin derivatives that crystallize in the tetragonal crystal system. The compound, space group, a, c, and unit cell volume are listed for each member. Series a, the four-coordinate species, has H2TPP as the parent compound. The existence of the series is expected and solid solutions of H2TPP and the metallo derivatives listed are readily formed . All members of this series have Ruf core conformations with substantial displacements of the carbon atoms. The second series is a substantial series of five- or six-coordinate complexes of which [Sn(TPP)Cl2] is the prototypical ordered example with symmetry. We first concern ourselves with the subset that have been catalogued as having I4/m as the space group. The phenyl groups of adjacent I-centered molecules make equivalent ligand pockets above and below the porphyrin plane. The pocket size is adequate for small (mono- or diatomic) axial ligands. Most of the species listed in Table XXVI(b) are seen to be five-coordinate hence the complexes display disorder in the crystal and...

The allylation of cyclic acetates such as cyclopentenyl or cyclo-hexenyl and cycloheptenyl derivatives also has been widely studied. For exart ile, the allyl palladium chloride dimer (1) is a useful catalyst precursor in the kinetic resolution of 2-cyclohexenyl acetate using Trost s chiral ligands pockets in conjunction to the planar chirality of ferrocene (eq 46). 1 The conversion was stopped at 54%, which allowed high enantiomeric excess for both the alkylated derivative and the chiral allylic acetate. 

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